Wondering how to plan for things,,, expecting to refi out in 2 years or less.

Property taxes are a little on the high end IMO based on your monthly expected rent - I aim for about 1-1 of monthly rent, thereabouts - i.e. if a place rents for $1000/month I would be looking for annual property taxes of $1,000.

If the property is fixed up, then there is less chance of someone tripping over a broken sidewalk, electrocuting themselves on out-of-date wiring, or water heater exploding because of corrosion.Just a few thoughts.

I don’t expect to get a chance to make a second offer whether it’s buying directly from the seller or through an agent. 

I purchased a townhome with the expectation of either 1. renovating and reselling it or 2. renting it. 

I expect my rental income to cover mortgage payments of course, but I can also cover things as needed by pulling out or borrowing against my stock investments - so losing my active income source isn't a huge concern for me.

She said that if she pays to get it fixed, she expects to keep it. 

Class D,F should be all electric to minimize fire risks (leaving stove on etc) a Class A properly might expect a gas stove.

Even if the #s are good should I expect these properties to be less attractive to buyers because of the flood liability in the future?

If you have a C property in a C area expect to pay a lot as a % to manage.There is a near 100% chance I know of the property (and know the owner, what they paid, what it was offered at, when they bought it, etc.).